How ancient plaque helps to reveal the secrets of our ancestors

Health and Wellness 29. jan 2023 3 min Assistant professor Gabriele Scorrano Written by Eliza Brown

In recent years, improvement of ancient DNA methods – and especially integration of information about genes, protein and microbiomes – has given unprecedented insight into the past population dynamics of Homo sapiens. A new multiomics study of dental calculus of two post–Last Glacial Maximum individuals from San Teodoro Cave in Italy shows a diet rich in animal protein, which is also reflected in the composition of the microbiome. The researchers expect future studies will enable much more holistic understanding of the dynamics and ecology of the past.

Despite their vulnerability to sugar and starchy foods in life, your teeth will survive long after you are gone – and may even reveal secrets to your distant descendants.

New research, published in November in Communications Biology, uses a decidedly unglamorous tool to determine what ancient humans ate – dental calculus, a hard, mineral build-up that forms on teeth when plaque takes up permanent residence on the tooth. Scientists have found that dental calculus acts like a multilayered time capsule, trapping microscopic proteins from food and preserving them for the ages.

The insight from analysing dental calculus are not limited to diet, emphasises co-author Gabriele Scorrano, a molecular anthropologist and Assistant Professor at the University of Copenhagen’s Globe Institute. The findings in dental calculus can also teach us about migration patterns and cultural interactions.

Grotta di San Teodoro

On a rocky Sicilian hill near the Tyrrhenian coast is a cave that people have visited for millennia. Now the San Teodoro Cave is a popular tourist destination surrounded by citrus groves and olive trees, but about 10,000–20,000 years ago it was a shelter frequented by ancient people. (Rewind to 30,000 years ago, and the area was home to Sicilian dwarf elephants, just under a metre tall, and a huge lake where giant hippopotamuses swam.)

Archaeologists have discovered the remains of at least seven humans in San Teodoro Cave. Radiocarbon dating situates them in the Upper Palaeolithic Era, also called the Old Stone Age, about 15,000 years ago.

We know the general shape of their lives – the people of the Palaeolithic Era were nomadic hunter-gatherers, migrating to follow prey and more favourable living conditions. Researchers think that Sicily might have been a refuge for ancient people driven south during the last big Ice Age. But by analysing the proteins trapped in their dental calculus, a team of researchers from Denmark and Italy hoped to learn more about what they ate – and who they interacted with.

Got milk?

The researchers scraped dental calculus from the partial remains of two people found in San Teodoro Cave – ST3, an adult man whose only earthly remains are his skull and part of an arm bone; and ST5, an individual believed to be female whose cranial cavity, partial jaw and fragmented arm bones survived.

Although the amount of dental calculus on ST3 and ST5 would not be remarkable for a modern human with all our sugared drinks and starches, these two had poor dental hygiene for their time. “In the Upper Palaeolithic Era, it is not common to find dental calculus because they normally eat meat as a main food source,” Gabriele Scorrano explains.

Most previous work with dental calculus focused on looking for milk proteins – a key marker for animal domestication, Gabriele Scorrano explains. But this time, the team broadened their scope and compared protein samples against a genetic database of plants and animals that these ancient Sicilians could have had for dinner.

Perplexing ibex

Gabriele Scorrano and his collaborators got an unprecedented sneak peek into the ancient Sicilians’ menu, from wild peas to wild boar. (They did not, as it were, get milk.)

Although some of the genetic hits seemed to be misfires (including a match with chickpeas, which were not cultivated until nearly 7,000 years later), the researchers identified proteins from extinct ancestors of cattle, wild boar and the European wild ass (hydruntine). That is in accordance with the palaeontological evidence, since bones from all three species were found in the Cave.

The researchers were excited to confirm that hunter-gatherers in Sicily ate fish. Small wonder – the Cave is within a stone’s throw of two rivers, and seafood is a staple of modern Sicilian cuisine today, but direct evidence has eluded archaeologists because tiny fish bones are not preserved well in the fossil record. Both ST3 and ST5 had dined on common carp, while ST5’s dental calculus also contained proteins that match a small shark species.

Gabriele Scorrano says the greatest revelation for the team was the genetic signature of the ibex – a goat-like creature that palaeontologists are certain was not a natural resident of Sicily.

However, the ibex was native to mainland Italy. There are only a few possible explanations, Gabriele Scorrano says – the people in San Teodoro could have travelled from mainland Italy to Sicily during their lifetimes, an enterprising hunter-gatherer somehow brought an ibex to Sicily or there was a trade relationship between two distinct communities.

“This was information we did not expect to find,” Gabriele Scorrano explains. “You can even use proteins in dental calculus to determine contact between or immigration of populations.”

“If you find proteins from species that you know were not present at that time in this specific place, they came from abroad,” he explains.

The future of molecular dentistry

Gabriele Scorrano and his team say that their results from the San Teodoro Cave are a strong proof of concept for the power of analysing the proteins trapped in dental calculus.

The first “toothbrushes” archaeologists have been able to document did not emerge until about 3,500 BCE in Egypt and Babylon, but researchers believe that the desire to remove things stuck in your teeth predates Homo sapiens. (Even great apes today have been observed using sticks as toothpicks and blades of grass as crude dental floss.)

Plaque and dental calculus really hit their stride with the advent of farming, when carbohydrate first comprised most of our diet. “You can see really huge quantities of dental calculus in many individuals after the introduction of agriculture,” Gabriele Scorrano says. “I do not think they used anything to clean their teeth.”

Their dental hygiene loss is our scientific gain – Gabriele Scorrano thinks that the techniques developed by his team could be applied to countless other ancient remains across the world, if some teeth survived and their owners were not oral hygiene prodigies. Analysing DNA and protein in concert make the insight into the ancients’ lives greater than the sum of their parts, Gabriele Scorrano emphasises. “One plus one is more than two,” he says.

Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave” has been published in Communications Biology. This project was supported by the Lundbeck Foundation, the Wellcome Trust and the Novo Nordisk Foundation. Several co-authors are affiliated with the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, which is also funded in part by the Foundation.

The Section for GeoGenetics operates in the cross-field between genetics, geology and archaeology. The section uses genomic, metagenomic and mineral...

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